Methods for detection and characterization of anti-viral vector antibodies

Abstract

Surface plasmon resonance-based methods for detecting and characterizing preexisting and/or treatment-induced anti-viral vector antibodies against viral vector-based gene therapy compositions in a biological sample from a subject are described.

We claim: 
     
         1 . A method for detecting an anti-viral vector antibody, the method comprising:
 incubating a mixture that comprises a viral vector and a biological sample suspected of containing an anti-viral vector antibody against the viral vector;   contacting the mixture with a ligand for the viral vector; and   using surface plasmon resonance (SPR) sensor chip to determine the extent to which the viral vector associates with the ligand following said contacting step;   
       wherein association of the viral vector with the ligand is reduced in the presence of the anti-viral vector antibody. 
     
     
         2 . The method of  claim 1 , further comprising using SPR to determine association of the viral vector with the ligand in the presence of a negative control sample known to lack an anti-viral vector antibody against the viral vector, and comparing the association of the viral vector with the ligand in the presence of the biological sample to that in the presence of the negative control sample. 
     
     
         3 . The method of  claim 1 , wherein the anti-viral vector antibody is a neutralizing antibody. 
     
     
         4 . The method of  claim 1 , wherein the anti-viral vector antibody is an immunoglobin (Ig) of class A (IgA), class D (IgD), class E (IgE), class G (IgG) or class M (IgM). 
     
     
         5 . (canceled) 
     
     
         6 . The method of  claim 3 , further comprising contacting the mixture with a complement system protein that is capable of binding to the anti-viral vector antibody associated with the viral vector covalently immobilized on the SPR sensor chip, wherein the complement system protein is C1q. 
     
     
         7 . (canceled) 
     
     
         8 . The method of  claim 6 , further comprising determining binding level of the complement system protein to the anti-viral vector antibody associated with the viral vector, wherein the binding level is indicative of the level of activation of the complement system. 
     
     
         9 . The method of  claim 1 , wherein the viral vector is an adeno-associated viral vector selected from the group consisting of AAV1, AAV2, AAV4, AAV5, AAV6, AAV7, AAV8, and AAV9. 
     
     
         10 . (canceled) 
     
     
         11 . (canceled) 
     
     
         12 . The method of  claim 1 , wherein the viral vector comprises a reporter selected from the group consisting of a fluorescent, a colorimetric, and a chemiluminescent reporter. 
     
     
         13 . (canceled) 
     
     
         14 . The method of  claim 12 , wherein the reporter is luciferase. 
     
     
         15 . The method of  claim 1 , wherein using SPR comprises determining a rate of association of the viral vector to the ligand, determining a binding affinity of the viral vector to the ligand, determining a rate of dissociation of the viral vector and the ligand, and/or determining a rate of regeneration of a ligand. 
     
     
         16 . (canceled) 
     
     
         17 . (canceled) 
     
     
         18 . The method of  claim 1 , wherein the biological sample is serum, plasma, whole blood, umbilical cord blood, cerebrospinal fluid, intraocular fluid, synovial fluid, saliva, bronchial fluid, alveolar fluid, gastrointestinal lavage fluids, or urine, optionally, wherein the biological sample is a diluted biological sample. 
     
     
         19 . The method of  claim 1 , wherein the ligand is immobilized on a solid support covalently or by affinity binding and the mixture is flowed over the solid support. 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . The method of  claim 19 , wherein the solid support comprises long and/or short chain dextran, carboxymethyl dextran, alginate, immobilized streptavidin, immobilized Protein A, or immobilized nitrilotriacetic acid (NTA). 
     
     
         23 . The method of  claim 1 , wherein the ligand is laminin receptor, heparan sulfate proteoglycans, AAV receptor or an antibody specific to the viral vector. 
     
     
         24 . The method of  claim 1 , further comprising using SPR to determine association of the viral vector with the ligand in the presence of a positive control sample known to comprise an anti-viral vector antibody, and comparing the association of the viral vector with the ligand in the presence of the biological sample to the association of the viral vector with the ligand in the presence of the positive control sample, optionally, wherein the positive control sample comprises a purified anti-viral vector antibody of known titer, of known affinity for the viral vector, or of known avidity for the viral vector. 
     
     
         25 . (canceled) 
     
     
         26 . (canceled) 
     
     
         27 . (canceled) 
     
     
         28 . The method of  claim 24 , wherein comparing the association of the viral vector with the ligand in the presence of the biological sample to that in the presence of the positive control sample results in a quantitative measurement of the presence of an anti-viral vector antibody against the viral vector in the biological sample. 
     
     
         29 . The method of  claim 1 , wherein using surface plasmon resonance to determine association of the viral vector with the ligand comprises assessing inhibition of the association by the anti-viral vector antibody in the biological sample or in the positive control sample based on maximal binding of the viral vector (Rmax) values measured for a plurality of dilutions of the biological sample or the control sample. 
     
     
         30 . A method comprising:
 obtaining a biological sample from each of multiple subjects suspected to be in need of treatment with a viral vector-based gene therapy composition;   performing the method according to  claim 1  on the biological sample; and   stratifying the subjects based on the presence of the anti-viral vector antibody in the biological sample.   
     
     
         31 . The method of  claim 30 , wherein the subjects having the biological sample determined to be negative for the anti-viral vector antibody or below a predetermined threshold for anti-viral vector antibody are selected for treatment with the viral vector-based gene therapy composition, and, optionally, excluding from treatment with the viral vector-based gene therapy composition subjects having the biological sample determined to be positive for or above a predetermined threshold for the anti-viral vector antibody. 
     
     
         32 . (canceled) 
     
     
         33 . The method of  claim 31 , wherein the method comprises providing a companion diagnostic for use with the viral vector-based gene therapy composition.